Marvel would have to deal with suddenly having all these big cities appear out of nowhere.

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Why? From their perspective those cities would have always been there. Once they merged they would have a shared history and geography.

What about the possibility of having different races of Atlanteans cohabiting and perhaps fighting over a combined Atlantis?

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DC already did that with Poseidonis (Aquaman) vs Tritonis. Lori Lemaris). The blue Atlanteans would just be another group.(Neptunis???}

I actually played around with this idea a few years back

THE DC_MARVEL CHRONOLOGY​

PRE-BIG BANG- The End of the First World. Galen from the planet Taa is absorbed by the Cosmic Egg that the Universe is collapsing into.

20 BILLION YEARS AGO: The Big Bang. The Universe/The Source is born. Eternity, Infinity, Chaos, Order and the Endless are born.

18 BILLION YEARS AGO: The God World forms. It is home to the Elder Gods of the Second World.

15 BILLION YEARS AGO: The War in Heaven, God World is destroyed sending out the Godwave. As the Godwave spreads across the Universe, Gods arise.

10 BILLION YEARS AGO- Sentient life evolves on the planet Maltus.

8 BILLION YEARS AGO- Galen, now called Galactus is reborn
Eon, a sentient quasi-physical entity is created by Eternity to become the cosmic custodian of the universe

4.8 BILLION YEARS AGO: Apokolips and New Genesis form from the shattered remains of God World

5 BILLION YEARS AGO- On Maltus the scientist Krona attempts to discover the beginning of the Universe. This causes a disruption in the Universal balance. To combat this the Maltusian decide to take action, but they cannot agree on what action. Some feel they must form a group of guardian to restore the balance. Others feel they must try and create beings who will restore the balance. A third group feels they can only watch and let things fix themselves.

The first group moves to Oa and became the Guardians of the Universe

The second calls themselves the Celestials and travel from world to world testing and experimenting on their inhabitants.

The third group is called the Watchers

The Sol System and Earth are formed.

Several immortals, from various worlds begin to call themselves the Elders of the Universe.

Eon, sensing the universal unbalance, appoints the first Protector of the Universe granting him the quantum power bands

3 BILLION YEARS AGO- The Guardians create the Manhunters. When the Manhunters fail, the Guardians create the Green Lantern Corps.

A group of Guardians with a more proactive approach split and form the Controllers.

2 BILLION YEARS AGO- The female Guardians leave and form the Zamarons.

On Earth Gaea gives birth to Atum. Atum sensing the Elder Gods have turned evil seeks to eradicate them. Many flee to other dimensions to escape.

I BILLION YEARS AGO- In one such dimension, Darkworld, an Elder God spawns a new race of Gods: Weaver, guardian & master of multi-colored threads of magical energy; Chaon, twisted god of evil & chaos; Gemimn, goddess of order; Tynan, cosmic balancer of order & chaos; Deedra, goddess of nature; and Jheryl, goddess of truth & knowledge.

The first of Earths Elemental are created.

500 MILLION YEARS AGO: Earth,the first insects.

245-65 MILLION YEARS AGO: Dinosaurs rule the Earth (Mesozoic Era).

200 MILLION YEARS AGO: Earth, the first mammals.

65 MILLION YEARS AGO- Earth, the Dinosaurs die out.

MILLIONS OF YEARS AGO- The Celestials perform experiments on the inhabitants of Skrullos, giving them their shape shifting abilities.

Over the next millennia The Skrulls create a star-spanning Empire with outposts from the Andromeda Galaxy to the Milky Way.

The Skrulls discover two sentient races on the planet Hala: the Kree and the Cotati. They set up s completion to see which one can join the Skrull Empire. The Skrulls choose the Cotati and the enraged Kree kill the Skrulls and take their technology.
Over the next centuries the Kree use the stolen technology to build their own empire and eventually attack the Skrulls, setting off the Kree-Skrull War.

The First Host of the Celestials arrives on Krypton. They create Kryptonian Eternals and Deviants. After a long war the Kryptonian Deviants are exiled beyond the borders of the now galactic Kryptonian Empire.

The Kryptonian Deviants wander into Skrull space and are enslaved. Millennia later their Skrull-Kryptonian descendents leave the empire en mass on an exodus that leads them to the planet Mars.

1 MILLION YEARS AGO- The First Host of the Celestials arrive on Earth and begin experimenting on the primitive proto hominids there. This gives rise to the Eternals and the Deviant sub-species. The Celestials also leave a modification in the genetic code of the proto-Hominids called a metagene. When activated by exotic energy, this gene can cause various physiological transformations.

One group of Eternals founds the City of the Golden Gate on the Continent of Atlantis. This gives rise to the Atlantean Empire which spreads over the Earth. The Atlanteans discover magic and begin to worship the Darkworld Pantheon.

900,000 YEARS AGO- The Kree create the Intelligence Supreme in response to the Skrulls creating a Cosmic Cube.

200,000 YEARS AGO- Homo Sapiens first appear on Earth.

50,000 YEARS AGO- A radiation from a meteor strike on Earth grants immortality to Cro-Magnons Vandar Ag (Vandal Savage) and Klarn (The Immortal Man)

Atlanteans launch their first interstellar craft.

The Celestial Second Host arrives on Krypton and the Kryptonians rise up against them. The Celestials break the Kryptonian Empire shattering it into a million pieces scattered throughout the Universe. Its remnants found on worlds like Daxam, Stronia, Yttrium and Dakkam. The Kryptonians are stripped of their Eternal powers and confined to Krypton.

45,000 YEARS AGO- Much of the Atlantean Continent is sunk following a metor strike. The City of the Golden Gate is destroyed. Survivors found new cities on other continents.

35,000 YEARS AGO- The Godwave energy, tapping into the minds of nascent Homo Sapiens species creates new Pantheons of Gods, giving rise to the Third World.

30,000 YEARS AGO- The Godwave energy returns to its source and New Gods arise on New Genesis and Apokolips. The beginning of the Fourth World.

25,000 YEARS AGO- Two factions of Eternals go to war. The losing faction leaves Earth but crashes on Uranus. On Uranus the Eternals find a Kree weapons depot and defeat the Sentry guarding it. Using Kree technology the repair their ship and head back to Earth. The Kree intercept the Eternal ship and capture several Eternals. The survivors manage to found a colony on Titan.
The Kree dissect their Eternal captives and discover the Celestials handiwork. They send a ship to Earth and perform their own genetic experiments on humans, giving rise to the Inhumans.

20,000 YEARS AGO- Humans begin migrating to the remnants of the continent of Atlantis.

18,000 YEARS AGO- The Deviants conquer Atlantis’s Lemurian colony in the Pacific.

16,000 YEARS AGO- The Celestial Second Host arrives on Earth. They sink Deviant Lemuria and the rest of Atlantis in the Great Deluge. The Atlanean cities of Posidonis, Tritonis and Nethria survive, as does a colony in the Arctic. Using both magic and science the surviving Atlanteans adapt to life under the sea.

The Eternals retreat to their hidden mountain refuges, limiting their interactions with humans.

The Guardians try to contain all magical energy into the Starheart and cast it into deep space.

7000 BCE- In Canaan a young boy named Jebediah is granted the powers of the Gods to use in the defense of his people.
The repentant fallen Angel Atzar becomes the Wrath of God.

6000 BCE- Egyptians begin to worship Atum-Ra.

6500 BCE-The God Poseidon makes himself known to the Atlantean survivors, who begin to worship him.

3500 BCE- Nabu, a Lord of Order arrives on Earth and becomes an advisor to various rulers in Mesopotamia and Egypt.

Jebediah of Canaan becomes the Sorcerer Supreme, taking the name Shazam.

4000 BCE- Zeus begins to seek worshipers on Earth

2950 BCE- Rama-Tut arrives from the future and proclaims himself Pharaoh. He forced to flee when four visitors from the future defeat him

2900s BCE- The mutant En Sabah Nur is born and is worshiped as a God by the Egyptians.

1500s BCE- The first of the Asgardian Gods makes himself known to humans

1200s BCE- Shazam grants Teth-Adam of Khandaq the power of the Gods.

Egyptian Prince Khufu discovers Nth metal in a crashed Thanagarian spaceship. Khufu and his wife Chay-era are slain by the Priest Hath-Set

Nabu, Shazam and Anath-Na Mut, advisors to Pharaoh, are bested by the Hebrew leader Moses who demands Ramses II frees his people. Pharaoh banishes all three. Nabu enters hibernation in the Valley of Ur. Shazam retires to Khandaq. Anath-Na Mut wanders the desert till he finds an ancient temple housing the Stone of Ka.

The Amazons are created by the Greek Goddesses

The Atlanteans emerge from the seas and attempt to conquer the surface world. Heroes from the four corners of the world band together to defeat them including Hippolyte of the Amazons, the Greek demi-god Heracles, Teth-Adam, Shazam and the Eternal Gilgamesh.

Hippolyta and Heracles begin an ill fated romace.

The Trojan War

The Amazons are banished to Themyscira after failing to fulfill the wishes of the Goddesses.

700s BCE- Rome is founded

1st Century BCE- A meteor containing the Starheart crashes to Earth in China

6th Century CE- Arthur of Britain forms the Knights of the Round Table who’s membership includes The Black Knight (Sir Percy of Scandia), The Shining Knight (Sir Justin of Cardiff) and the Silent Knight ( Sir Brian of Kent) Merlin brings forth the Demon Etrigan, who takes the human form of Jason Blood.

14th Century CE- Shazam appoints the Ancient One the new Sorcerer Supreme.

1878-A band of cowboys prevent Kang the Conqueror from taking over 19th Century America: Jonah Hex, the Two Gun Kid, Bat Lash, the Rawhide Kid, Nighthawk, the Phantom Rider and Scalphunter are among the participants.

Marvel would have to deal with suddenly having all these big cities appear out of nowhere.

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No problem there. Not like there was anything in Jersey or Delaware anyway. Also gonna have entire countries popping up, like Latveria and the gorilla empire.

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Marvel has a few fake cities of its own. There was a city introduced in Spider-Man as the home of one of Spidey's nineties villains callled "Fireheart, New Mexico." (The villain was like Bruce Wayne with the Cheetah's powers.) Also, for the first two issues of their comic the Fantastic Four were based in "Central City." ( I smell an FF/Flash crossover! The FFF?)

One of the things I think would've been cool is if President Luthor had appointed Norman Osborn as head of SHIELD/HAMMER. In retrospect I wish DC had been thinking more along the Dark Reign lines as fully as Marvel did when Lex became president.

Also, Amanda Waller knocking heads with Luke Cage on a Thunderbolts/Suicide Squad team would be interesting.

A Black Panther-Vixen romance. Or Catman (Secret Six version) v. Black Panther would be pretty cool. As would a Bronze Tiger v. Panther match up.

Well, Batman and Lex Luthor would probably lose their "Smartest Men on Earth" title when they have to co-exist with Reed Richards, Dr Doom, Hank Pym, Tony Stark, Bruce Banner, T'Challa, etc.

In fact, I'd like to see Lex Luthor and Dr Doom as arch-rivals.

I'd think Batman would be the one trying to neutralize Stark Industries TBH. He wouldn't like the idea of a loose cannon like Stark producing weapons like the Iron Man suit for anyone. But then after the Obadiah Stane thing he realizes Tony is the better one in charge and lays off.

Would Marvel heroes join the Justice League? Or would they continue in their own groups, like the Avengers?

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Both teams have changed rosters many times, so I'm sure there'd be some intermingling if they coexisted. Although the thing is, they both fill the same basic role in the superheroic ecosystem, as it were -- the all-star team that comes together for the crises too big for any one hero. So if the characters had coexisted all along, I'm not sure we would've had separate Avengers and JL teams, but one team that emerged as an amalgam of the two (pardon the expression). Either that, or one team would dominate as the heavy-hitter roster with folks like Superman, Captain America, Wonder Woman, Iron Man, Green Lantern, and Thor, and the other might be more a second-stringer team akin to the West Coast Avengers or Justice League Europe.